using GOToolBox for the analysis of the functional evolution of

Bernard jacq at lgpd.univ-mrs.fr
Fri Jan 21 09:58:16 EST 2005



 Dear colleagues,


 This short mail to inform the community of researchers interested in
molecular evolution of the availability of GOToolBox, a series of
programs using Gene ontology that we published recently in Genome
biology
(http://www.biomedcentral.com/content/pdf/gb-2004-5-12-r101.pdf).

 GOToolBox can be useful to analyse groups of genes derived from
microarrays,Chromatin-Immunoprecipitations, from the analysis of
protein-protein (two-hybrid), protein_DNA and/or genetic networks. It
can also be used to study thefunctional evolution of genes (see
below).

The programs from GOToolBox are directly accessible through a Web
site described in the article.

 GOToolBox performs five main tasks:

 - gene dataset creation,
 - selection and fitting of GO terms at a given ontology level (GO-Diet),
 - statistical analysis of GO terms associated with gene sets
(GO-Stats) in order to find over- or under-represented terms,
 - GO-based gene clustering (GO-Proxy) allowing to find sub-groups of
functionnally related genes within a gene set,
 - gene retrieval based on GO annotation similarity (GO-Family) in
one or several species.

 Other developments are presently on their way.

 At the moment, GOToolBox supports analyses of GO terms for six species :
Yeast (Sc), Arabidopsis, Drosophila, nematode, mouse and humans.

 As an example of the use of GOToolbox in the molecular evolution
field, we recently published analysis of yeast duplicated genes using
protein-protein interactions and GO annotation
(http://www.biomedcentral.com/content/pdf/gb-2004-5-10-r76.pdf)

 For the authors,

 David Martin and Bernard Jacq

Bernard Jacq
LGPD-IBDM
Parc Scientifique de luminy
13288 Marseille Cedex 9

tel (33) 04 91 82 94 25
fax (33) 04 91 82 06 82


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